SMARTSViewer
StreamableVernalis custom KNIME nodes package version 1.12.0.v201708101336 by Vernalis (R&D), UK
K. Schomburg, H.-C. Ehrlich, K. Stierand, M.Rarey; From Structure Diagrams to Visual Chemical Patterns, J. Chem. Inf. Model., 2010, 50, pp 1529-1535
The Communication Error Settings tab allows setting of behaviour relating to server communication problem handling. The values set are applied to each row in turn. The server will only be contacted until a successful result is returned. The settings allow the user to control the behaviour of the node should the SMARTSviewer server be functioning incorrectly. Note that it is not currently possible to cancel execution during a row, so use long delay settings with care!
Note that SMARTs strings are transferred to the remote server unencrypted, and the the server maintains an anonymous record of query SMARTs strings to aid future development.
This node was developed by Vernalis (Cambridge, UK). For feedback and more information, please contact knime@vernalis.com
Options
- Select a column containing the SMARTs Strings
- Select a column containing SMARTs strings for visualsation. No SMARTS validation is carried out prior to sending to the remote server, which will return a blank image for invalid SMARTS strings
- Select legend type
- Choose the desired legend type: Dynamic - detailed text description of each atom and bond; Static - short description of how each symbol is depicted in the visualisation
- Select Visualisation modus
- Element symbols uses text representation of the element symbols in the depiction
Communication Error Settings
- Number of retries to contact server
- Set the number of times the server will be re-contacted following a failure.
- Delay between attempts (secs)
- The delay period between each re-try
- Ignore server errors
- If set, the node will return a 'missing value' cell for each row which failed to contact the server after the defined number of attempts - allowing workflow execution to continue, otherwise node execution will fail. Setting a long delay interval (max 10 minutes) and large number of attempts (max 20) allows the workflow a chance to restore functionality (it will take over 3 hours between the first and last attempt for each row in these circumstances)
- Restore Defaults
- Restore the default server settings.
Input Ports
Output Ports
Best Friends (Incoming)
File Reader (31 %) SourceStreamable
CSV Reader (13 %) Source
Molecule Type Cast (13 %) ManipulatorStreamable
MarvinSketch (6 %) Source
Table Creator (6 %) Source
Column Rename (6 %) ManipulatorStreamable
Smiles Directory Reader (6 %) Source
Ring Descriptors (6 %) 
RDKit Canon SMILES (6 %) ManipulatorStreamable
RDKit MCS (6 %) Manipulator
SMARTSViewer (< 1 %) ManipulatorStreamable
MolConverter (< 1 %) ManipulatorStreamable
Row Filter (< 1 %) ManipulatorStreamable
Excel Reader (XLS)(< 1 %) SourceStreamableDeprecated
Substructure Search (< 1 %) Manipulator
RDKit Find Murcko Scaffolds (< 1 %) ManipulatorStreamable- Show all 16 recommendations
Best Friends (Outgoing)
Interactive Table (44 %) Visualizer- Molecule Type Cast (22 %) ManipulatorStreamable
- Empty Column Checker (11 %) Other
Table to PDF (11 %) Visualizer- SMARTS Query (11 %) Manipulator
- SMARTSViewer (< 1 %) ManipulatorStreamable
K Nearest Neighbor (< 1 %) LearnerStreamable
RDKit Molecule Highlighting (< 1 %) ManipulatorStreamable- Show all 8 recommendations
Workflows
Update Site
To use this node in KNIME, install Vernalis custom KNIME nodes package from the following update site: